What We Lost
by poetrygrrl39
Summary: The continuation of my Helen Magnus and Daniel Jackson crossover series, continuing from You Found Me. Helen and Daniel try to maintain their relationship in the face of challenges both unique to the Sanctuary and universal everywhere.
1. Prologue

_I have hesitated to continue this storyline, because it has become so completely AU in that Ashley Magnus has been killed off (which, btw, sucky decision SyFy, thanks). I suppose this is what I get for being unspoiled and assuming they weren't going to kill off Ashley._

_And now that Michael Shanks is guest starring (and looking adorably scruffy in the preview), I was even more uncertain._

_However, I have decided to continue despite these issues. Please read _Lost and Found_ and _You Found Me_ before reading this story, or it will make no sense._

_In any case….._

_On with the show!_

**What We Lost**

**Prologue**

Helen slammed the door behind her with a crash that rattled the paintings on the wall, stomping furiously to her desk and flinging her backpack into her chair. She was holding on to the edges of the desk, head down, trying to calm her breathing, when she heard the door swing open behind her and slam back shut. Breathing forgotten, she swung around with a roar.

"How dare you! Get out of here!"

Daniel Jackson stood facing her, hands on his hips, glaring.

"I am not leaving until you talk to me."

"I don't want to talk to you, I don't even want to look at you! I would have assumed that was obvious when I told you to leave me the hell alone!"

"Damnit Helen, you can't shut me out like this."

"The hell I can't!" she screamed back. She spun away from him, marching over to the window and staring unseeing at the view, hands clenching and unclenching, desperately trying to get her temper under control.

Her effort wasn't helped by the fact that she could feel Daniel's stare burning into the back of her head, feel the frustration, confusion and concern radiating from him. For a man who had been a diplomat, he certainly had no ability to contain his emotions, she thought bitterly.

She heard him move across the room, felt the heat from him as he stood behind her, not touching her, but within a whisper of doing so.

"Helen, please," he murmured.

She spun on her heel, intending to blister him with a clear explanation of every one of his shortcomings, and stopped with her mouth open, caught firmly by the tears standing in his eyes, and the bruise forming on his right cheekbone.

"I'm sorry, Helen," he whispered, hand coming up as if to touch her, then dropping to his side, clenched into a fist. "I have no idea what I've done to make you so angry, but I'm sorry."

Helen took the half step forward that put her in contact with him and buried her face in his chest, hands still hanging at her sides even as his arms came up around her.

What he had done was almost get himself killed, again. Another Abnormal, another day at the office, another brush with death for Daniel Jackson. It wasn't even that he was careless, although he sometimes took risks she didn't agree with. He just seemed to be a magnet for trouble.

Standing in the circle of Daniel's arms, listening to his heartbeat beneath her ear, Helen Magnus sighed deeply.

She had known that integrating Daniel into her life and her work was going to be challenging.

She had no idea it was going to tear her apart inside.

She had to end it, she thought sadly to herself. For his own safety, and for her own sanity.

The thought made her breath catch in her throat and brought her arms up to hold him as well, pulling him tightly against her, fighting tears.

For once in her very long life, Helen Magnus knew what she should do, what she had to do, but simply couldn't bring herself to do it.

Not today, at least.

She pulled back to look into Daniel's face and rose up to plant her lips against his, urgently. She wasn't surprised when he broke the kiss, gripping her upper arms.

"Helen, two minutes ago you were screaming at me, what's going on?"

She shrugged off his arms and unzipped her top, letting it fall open, not missing the catch in his breath as he stared down at her.

"I want to make up?" she asked, smiling at him as she pulled the elastic band from her hair, the strands falling loose.

"But I still have no idea what I did to make you so angry. Please, Helen, talk to me."

Helen, her open top framing the black lace of her bra, ran her hands up his chest.

"Daniel, I'm sorry I went so crazy. You...you scared me when that Abnormal took hold of you. I was terrified I was going to lose you," she kissed him again, noticing this time that he responded to her. "Please, Daniel, I need to know we're both alive."

Daniel blinked a few times and began kissing her in earnest.

More than an hour later, after they had made love slowly on the rug in front of the fire, Helen lay with her eyes closed, pretending to sleep. She felt Daniel lean over her, kissing her forehead, and whisper softly, "I love you, Helen."

She waited until he lay down next to her, spooning her beneath the blanket that had been draped over the couch, to let the tears slip from her eyes.

What the hell was she going to do? she thought despairingly. What the hell was she going to do?

Daniel, holding her to him, feeling the tension in her body and the wetness on his arm from where her tears had fallen, felt his heart sink. It had all started out so well, he thought. And now he could feel she was withdrawing, even clasped in his arms, she wasn't completely there. And he didn't know what to do any more than she did.

tbc...


	2. Chapter 1

_A/N: Super quick stop in SG1 territory, then off to the Sanctuary._

**What We Lost**

**Chapter 1**

_Two months earlier…_

Daniel Jackson had been surprised how easy it was to leave the Stargate program. True, there had been, as he anticipated, piles and piles of paperwork to sign indicating that he would never, ever, ever – upon penalty of very long prison sentences – tell anyone anything about the program. He had been debriefed almost to the point of preferring a cell at Guantanamo, but knowing that Helen was waiting for him had kept him in an optimistic frame of mind.

Two weeks after Helen had been rescued from her underground prison, he was officially out of the military and on his way to become part of the Sanctuary. He wondered about both living with and working with Helen Magnus and her team, but decided he would deal with any issues as they came.

At his going away party, Jack O'Neill had pulled him to the side.

"So, Space Monkey, Carter tells me that your friend Helen looks a lot like someone else we know."

Daniel shrugged one shoulder. "Why do you insist on calling her Carter, Jack? It's not like we all don't know you two are together."

"Don't change the subject, Danny," O'Neill snapped, although Daniel noticed with satisfaction that his friend was actually blushing. "I just think it's interesting that you travel all over the galaxy and you end up with a woman who looks just like your best female friend. Don't you think that's interesting, Mitchell?" Jack roared at the passing pilot, grabbing his arm and pulling him into the conversation.

Mitchell looked wild-eyed at the General and Daniel and mumbled something about needing another beer, handing the full glass he was carrying to Vala before beating a hasty retreat.

"Personally, General, I think it's fascinating that Daniel is running off with a woman at all," she leaned conspiratorially toward the general, making sure her breasts pressed into Daniel's upper arm, and stage whispered, "I always suspected he was gay, you know."

Daniel, who had been expecting her words, sighed and shrugged her off him. Jack, who obviously had not and was in the middle of a sip from his glass, actually sprayed beer on General Landry, who had wandered over to join the conversation. The general backed away, swearing and swiping at the front of his shirt.

"Yeah, Jack, didn't you know that all the rumors were that you and I…." Daniel didn't need to get any farther before Jack waved his arm at him, snarled something about having an early flight, and retreated, pulling Sam into a corner, talking for a few moments before kissing her in front of the entire room.

Vala goggled, Daniel smiled, and a returning Mitchell stared, gulped down the beer he was holding, and went back to the bar.

It was a direct result of all of Cam's trips to the bar that Daniel ended up in the backseat of Sam's car as she drove both him and Jack to catch their respective flights, rather than getting a lift from Mitchell as he had promised. She kept up a steady string of chatter that slowly died the closer they got to the airport.

Daniel unloaded his luggage from the trunk, allowing Jack and Sam to say a private goodbye. He walked slowly around the side of the car, hoping they were done, and found them in a tight embrace.

Sam released Jack and stepped over to Daniel, smiling tearfully at him.

"God, Daniel, I am going to miss you!" she said, pulling him into a hug.

"I'm only a phone call away, Sam. And it's not that far."

"I know, I know, I guess I just got used to the idea that you would always be at Stargate Command, that wherever I was sent, I could count on you being there. It's going to be hard to stop by there and not see you. Or call and not know you are working on whatever the latest crisis is."

Jack laughed behind Sam, sounding a little choked. "Trust me, Sam, he'll be finding a new crisis to keep him occupied wherever he goes."

Sam turned and shook a finger at Jack. "It's not the same, and you know it."

Jack nodded slowly. "Yeah. Yeah, I do know it, and I'm gonna miss you too, Danny Boy."

They engaged in a quick man hug, complete with back patting, then Daniel hugged Sam one more time before he headed toward the plane that would take him to his new life.

* * *

He wished two days later than Jack's prediction about Daniel finding a new crisis had been a little less accurate.

He had arrived to find a nearly empty Sanctuary, with only the Big Guy on site. Helen and her team had been called away to round up an Abnormal in Brazil.

Daniel had unpacked, wandered around, read books, perused the piles of information Helen had left him, and was on his third language lesson from the mermaid when the team came back. Henry was on a gurney, half in wolf form, being wheeled into the Shoe by two men Daniel didn't know, Ashley practically hysterical, Helen shouting orders and Will Zimmerman standing off to the side shaking his head and looking concerned.

"What the hell happened?" Daniel asked Will as the gurney went past them, Helen sending him a quick glance and a tight smile. They disappeared around the corner.

"Henry got bit by something out there, some kind of bug that looked like a whacked out firefly on crack," Will said. "He started changing without warning, without being able to control it. None of the meds Magnus had on hand did anything. And now, it's like he's stuck, half were-Henry and half human-Henry. He took a chunk out of Magnus, scratched the hell out of my shoulder, but thankfully had enough Henry left in him to not hurt Ashley."

Daniel turned to look at Will, noticing for the first time the bulk of bandages beneath his black t-shirt and the way he held his arm. "You okay?"

"Nothing several shots of morphine and some stitches couldn't fix. Magnus fixed me up."

Daniel opened his mouth to offer to help Will to his room, and his bed, which it desperately looked like the younger man needed, when he heard a scream and what sounded ominously like a body hitting a stone wall.

He took off at a sprint toward the sound, skidding to a halt about 20 feet away from an entirely werewolfed Henry, who was free of his restraints. He was looking in the opposite direction, toward the gurney.

"Daniel, don't move," he heard Helen say softly. He could just see her out of the corner of her eye, crouched near the overturned gurney, holding some kind of syringe. The body of one of the two men who had wheeled Henry in lay at the base of the wall to his left. As he watched, he could see that the man was breathing. He couldn't see Ashley or the other man and assumed they were hiding behind the tipped gurney.

A split second too late, Daniel remembered that Will was behind him, and the psychiatrist lurched into him, knocking him off balance and apparently drawing the attention of the werewolf, which opened his mouth with a saliva-spraying roar and charged.

Daniel braced himself, staying in front of the already injured Will, wondering if he was going to survive his first day here, when the werewolf yelped and stumbled, skidding to an unconscious halt at Daniel's feet, a syringe protruding from his neck.

He looked up from the tangled body, eyes wide, to see Helen looking at him, the same tight smile on her face that she had greeted him with.

"Welcome to the Sanctuary, Dr. Jackson," she said as Ashley clambered out from behind the gurney and cautiously approached her unconscious lover.

"You throw a welcome party like this for everyone?" he asked, steadying Will, who was swaying on his feet after ricocheting his injured shoulder off Daniel's back.

Helen gave a real smile. "You should see what we did for Will when he started, right, Will?"

Will snorted, and Daniel decided that maybe he didn't really want to know.

He didn't see much of Helen until the next day. She had worked round the clock to restore Henry to his normal form, which apparently involved the application of some kind of poison sucking slug and electroshock therapy, from the garbled explanation she gave him late the next night after she fell into his bed, too tired to even kiss him good night.

He smoothed her hair, carefully checked the bite mark on her arm, and pulled her close to him before falling asleep, feeling a little put out and angry at himself for feeling that way.

The fact that she woke him up the next morning with a toe-curling reenactment of one of their more explicit telephone calls made up for any slight he may have felt.

Life fell into a pattern over the next few days. During the day, Helen worked in her lab while Daniel worked his way through her library of information on Abnormals, starting with ancient history and working his way forward. He figured he could be of the most use to the Sanctuary by becoming an expert on the history, since Helen, Will and Ashley clearly had the present well in hand.

At night, he and Helen fell into one of their beds and often made love, sometimes just held each other, talking about something he had read or something she had found. Helen had insisted on keeping separate rooms.

"I'm afraid after all this time, I'm just not quite sure how to move someone else into my room," she said with a smile.

"Not to mention the closet space!" Daniel had said, also smiling, although he wondered if it was some kind of sign that she wasn't letting him all the way into her life.

He felt awkward at first, being included in staff meetings and family dinners, which, interestingly enough, usually featured the exact same people. He noticed, and appreciated, when Ashley made an effort to draw him into the conversations.

It was different, so very different, than Stargate Command, but also somehow the same. The military structure might be gone, conversations and discussions flying around the table without any kind of concern for who was in charge, no deference to Helen when there was disagreement, but they were a family, the way SG1 had been a family. Mismatched and odd, but a family all the same.

About 10 days after he joined the Sanctuary, Daniel was sitting in the office that had been designated as his, reading through a tome in Gaelic, when Will knocked and stuck his head in.

"Hey, Daniel, we've got an extraction and pickup. Magnus thought you might want to come."

Daniel slipped a marker into the book and dropped it on his desk. "Yes, please!"

Will smiled at his eagerness, knowing that the older man must be feeling a little stir crazy, and led the way to the armory.

tbc…..


End file.
